Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.

Analysis of the free vibration of rectangular plates with central cut-outs using the discrete Ritz method

We present an analysis of the free vibration of plates with internal discontinuities due to central cut-outs. A numerical formulation for a basic L-shaped element which is divided into appropriate sub-domains that are dependent upon the location of the cut-out is used as the basic building element. Trial functions formed to satisfy certain boundary conditions are employed to define the transverse deflection of each sub-domain. Mathematical treatments in terms of the continuities in displacement, slope, moment, and higher derivatives between the adjacent sub-domains are enforced at the interconnecting edges. The energy functional results, from the proper assembly of the coupled strain and kinetic energy contributions of each sub-domain, are minimized via the Ritz procedure to extract the vibration frequencies and. mode shapes of the plates. The procedures are demonstrated by considering plates with central cut-outs that are subjected to two types of boundary conditions. (C) 2003 Elsevier Ltd. All rights reserved.

A simple practical method for bulk and rapid extraction of free-living nematodes from marine and estuarine sediments

A simple, rapid method is described for the extraction of large numbers of free-living nematodes from estuarine sediments. This method does not physically or chemically alter or damage the nematodes, but instead relies on their downward movement through a filtering layer of double ply tissue paper and into aerated water-filled trays. Seven trials each with 10 trays kept at 25degreesC for an initial period of 24 h yielded 3985 live nematodes l(-1) (+/-511.5 standard deviation) of estuarine sediment, free of sediment and with minimal debris. Time effects were statistically significantly different, with the same 10 trays yielding another 1259 nematodes l(-1) (+/-413.4) when kept for a second period of 24 h at the same temperature. Temperature effects were also significant, and 7 trials each with 10 trays kept for 24 h at 20-21degreesC, produced a lower yield of 2160 nematodes l(-1) (+/-532.7) of sediment. The method is expected to be of use in nematode extractions from both estuarine and marine sediments.

A distributed equivalent magnetic current based FDTD method for the calculation of E-fields induced by gradient coils

This paper evaluates a new, low-frequency finite-difference time-domain method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretization of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modelling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multi-layered spherical phantom model and a complete body model. (C) 2004 Elsevier Inc. All rights reserved.

Postsynthesis stabilization of free-standing mesoporous silica films

Mixed ammonia-water vapor postsynthesis treatment provides a simple and convenient method for stabilizing mesostructured silica films. X-ray diffraction, transmission electron microscopy, nitrogen adsorption/desorption, and solid-state NMR (C-13, Si-29) were applied to study the effects of mixed ammonia-water vapor at 90 degreesC on the mesostructure of the films. An increased cross-linking of the silica network was observed. Subsequent calcination of the silica films was seen to cause a bimodal pore-size distribution, with an accompanying increase in the volume and surface area ratios of the primary (d = 3 nm) to secondary (d = 5-30 nm) pores. Additionally, mixed ammonia-water treatment was observed to cause a narrowing of the primary pore-size distribution. These findings have implications for thin film based applications and devices, such as sensors, membranes, or surfaces for heterogeneous catalysis.

Analysis of the effect of transverse modes on free-space optical interconnect performance

Vertical-cavity surface-emitting lasers (VCSELs) and microlenses can be used to implement free space optical interconnects (FSOIs) which do not suffer from the bandwidth limitations inherent in metallic interconnects. A comprehensive link equation describing the effects of both optical and electrical noise is introduced. We have evaluated FSOI performance by examining the following metrics: the space-bandwidth product (SBP), describing the density of channels and aggregate bandwidth that can be achieved, and the carrier-to-noise ratio (CNR), which represents the relative strength of the carrier signal. The mode expansion method (MEM) was used to account for the primary cause of optical noise: laser beam diffraction. While the literature commonly assumes an ideal single-mode laser beam, we consider the experimentally determined multimodal structure of a VCSEL beam in our calculations. It was found that maximum achievable interconnect length and density for a given CNR was significantly reduced when the higher order transverse modes were present in Simulations. However, the Simulations demonstrate that free-space optical interconnects are still a suitable solution for the communications bottleneck, despite the adverse effects introduced by transverse modes.

Effect of free ammonia and free nitrous acid concentration on the anabolic and catabolic processes of an enriched Nitrosomonas culture

The effects of free ammonia (FA; NH3) and free nitrous acid (FNA; HNO2) concentrations on the metabolisms of an enriched ammonia oxidizing bacteria (AOB) culture were investigated using a method allowing the decoupling of growth and energy generation processes. A lab-scale sequencing batch reactor (SBR) was operated for the enrichment of an AOB culture. Fluorescent in-situ hybridization (FISH) analysis showed that 82% of the bacterial population in the SBR bound to the NEU probe specifically designed for Nitrosomonas europaea. Batch tests were carried out to measure the oxygen and ammonium consumption rates by the culture at various FA and FNA levels, in the presence or absence of inorganic carbon (CO2, HCO3, and CO32-). It was revealed that FA of up to 16.0 mgNH(3)-N (.) L-1, which was the highest concentration used in this study, did not have any inhibitory effect on either the catabolic or anabolic processes of the Nitrosomonas culture. In contrast, FNA inhibited both the growth and energy production capabilities of the Nitrosomonas culture. The inhibition on growth initiated at approximately 0.10 mgHNO(2)-(NL-1)-L-., and the data suggested that the biosynthesis was completely stopped at an FNA concentration of 0.40 mgHNO(2)-N (.) L-1. The inhibition on energy generation initiated at a slightly lower level but the Nitrosomonas culture was still oxidizing ammonia at half of the maximum rate at an FNA concentration of 0.50-0.63 mgHNO(2)-N (.) L-1. The affinity constant of the Nitrosomonas culture with respect to ammonia was determined to be 0.36 mgNH3-N (.) L-1, independent of the presence or absence of inorganic carbon. (c) 2006 Wiley Periodicals, Inc.

Individual calibration for estimating free-living walking speed using the MTI monitor

Purpose: This study was conducted to devise a new individual calibration method to enhance MTI accelerometer estimation of free-living level walking speed. Method: Five female and five male middle-aged adults walked 400 m at 3.5, 4.5, and 5.5 km(.)h(-1), and 800 in at 6.5 km(.)h(-1) on an outdoor track, following a continuous protocol. Lap speed was controlled by a global positioning system (GPS) monitor. MTI counts-to-speed calibration equations were derived for each trial, for each subject for four such trials with each of four MTI, for each subject for the average MTI. and for the pooled data. Standard errors of the estimate (SEE) with and without individual calibration were compared. To assess accuracy of prediction of free-living walking speed, subjects also completed a self-paced, brisk 3-km walk wearing one of the four MTI, and differences between actual and predicted walking speed with and without individual calibration were examined. Results: Correlations between MTI counts and walking speed were 0.90 without individual calibration, 0.98 with individual calibration for the average MTI. and 0.99 with individual calibration for a specific MTI. The SEE (mean +/- SD) was 0.58 +/- 0.30 km(.)h(-1) without individual calibration, 0.19 +/- 0.09 km h(-1) with individual calibration for the average MTI monitor, and 0.16 +/- 0.08 km(.)h(-1) with individual calibration for a specific MTI monitor. The difference between actual and predicted walking speed on the brisk 3-km walk was 0.06 +/- 0.25 km(.)h(-1) using individual calibration and 0.28 +/- 0.63 km(.)h(-1) without individual calibration (for specific accelerometers). Conclusion: MTI accuracy in predicting walking speed without individual calibration might be sufficient for population-based studies but not for intervention trials. This individual calibration method will substantially increase precision of walking speed predicted from MTI counts.

The inhibitory effects of free nitrous acid on the energy generation and growth processes of an enriched Nitrobacter culture

The inhibitory effects of nitrite (NO2-)/free nitrous acid (HNO2-FNA) on the metabolism of Nitrobacter were investigated using a method allowing the decoupling of the growth and energy generation processes. A lab-scale sequencing batch reactor was operated for the enrichment of a Nitrobacter culture. Fluorescent in situ hybridization (FISH) analysis showed that 73% of the bacterial population was Nitrobacter. Batch tests were carried out to assess the oxygen and nitrite consumption rates of the enriched culture at low and high nitrite levels, in the presence or absence of inorganic carbon. It was observed that in the absence of CO2, the Nitrobacter culture was able to oxidize nitrite at a rate that is 76% of that in the presence of CO2, with an oxygen consumption rate that is 85% of that measured in the presence of CO2. This enabled the impacts of nitrite/FNA on the catabolic and anabolic processes of Nitrobacter to be assessed separately. FNA rather than nitrite was likely the actual inhibitor to the Nitrobacter metabolism. It was revealed that FNA of up to 0.05 mg HNO2-N center dot L-1 (3.4 mu M), which was the highest FNA concentration used in this study, did not have any inhibitory effect on the catabolic processes of Nitrobacter. However, FNA initiated its inhibition to the anabolic processes of Nitrobacter at approximately 0.011 mg HNO2-N center dot L-1 (0.8 mu M), and completely stopped biomass synthesis at a concentration of approximately 0.023 mg HNO2-N center dot L-1 (1.6 mu M). The inhibitory effect could be described by an empirical inhibitory model proposed in this paper, but the underlying mechanisms remain to be revealed.

An equivalent distributed magnetic current based FDTD method for the calculation of e-fields induced by gradient coils in MRI

This paper evaluates a low-frequency FDTD method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current (DEMC) is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretizing of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modeling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multilayered spherical phantom model and a complete body model.